Chlorine in PDB 3rmo: Human Thrombin in Complex with MI004

All present enzymatic activity of Human Thrombin in Complex with MI004:
3.4.21.5;

The structure of Human Thrombin in Complex with MI004, PDB code: 3rmo was solved by A.Biela, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.74 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.120, 71.030, 72.750, 90.00, 100.40, 90.00
R / Rfree (%)	13.4 / 16.5

The structure of Human Thrombin in Complex with MI004 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Human Thrombin in Complex with MI004 (pdb code 3rmo). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Human Thrombin in Complex with MI004, PDB code: 3rmo:

Chlorine binding site 1 out of 1 in the Human Thrombin in Complex with MI004


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Thrombin in Complex with MI004 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl1 b:11.0 occ:1.00 CL3 H:S041 0.0 11.0 1.0 C31 H:S041 1.8 11.2 1.0 C33 H:S041 2.7 11.3 1.0 C30 H:S041 2.7 12.6 1.0 O H:TRP215 3.4 10.7 1.0 O H:PHE227 3.4 9.0 1.0 N H:PHE227 3.6 8.9 1.0 CA H:GLY226 3.6 10.6 1.0 CG1 H:VAL213 3.8 10.1 1.0 CZ H:TYR228 3.9 8.9 1.0 C H:TRP215 3.9 9.8 1.0 N H:TRP215 3.9 9.5 1.0 C H:GLY226 3.9 10.1 1.0 CB H:ALA190 3.9 13.1 1.0 OH H:TYR228 4.0 10.6 1.0 N H:SER214 4.0 8.8 1.0 C26 H:S041 4.0 11.9 1.0 C29 H:S041 4.0 12.5 1.0 CE2 H:TYR228 4.1 9.4 1.0 C H:PHE227 4.2 9.1 1.0 CE1 H:TYR228 4.2 8.8 1.0 CA H:TRP215 4.4 9.7 1.0 OD1 H:ASP189 4.4 12.9 1.0 CA H:PHE227 4.5 8.7 1.0 CA H:VAL213 4.5 8.3 1.0 C27 H:S041 4.5 12.9 1.0 C H:SER214 4.5 8.5 1.0 CD2 H:TYR228 4.6 7.9 1.0 C H:VAL213 4.6 8.3 1.0 N H:GLY216 4.7 11.4 1.0 CB H:VAL213 4.7 9.5 1.0 CD1 H:TYR228 4.7 8.4 1.0 O H:HOH1082 4.8 12.0 1.0 CA H:SER214 4.9 8.6 1.0 O H:GLY226 4.9 10.3 1.0 CG H:TYR228 4.9 7.7 1.0

A.Biela, F.Sielaff, F.Terwesten, A.Heine, T.Steinmetzer, G.Klebe. Ligand Binding Stepwise Disrupts Water Network in Thrombin: Enthalpic and Entropic Changes Reveal Classical Hydrophobic Effect J.Med.Chem. V. 55 6094 2012.
ISSN: ISSN 0022-2623
PubMed: 22612268
DOI: 10.1021/JM300337Q